基于GenBank 数据对红柴胡nrDNA序列ITS2片段的分析
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摘要
[目的]了解红柴胡nrDNA序列ITS2片段特征,为中药柴胡的分子鉴定提供科学依据。[方法]从GenBank中获取已公布红柴胡ITS全长序列38条和ITS2序列3条,利用MEGA6.0进行多序列比对,分析ITS2片段碱基成分、变异位点、信息位点,计算遗传距离,并用邻接法(NJ)构建系统聚类树。[结果]ITS2片段长度为224～230 bp,共发现14个简约信息位点,最大遗传距离0.124,系统树可明显分为4组,85.37%的聚为一组。[结论]ITS2在红柴胡居群中比较保守,可作为DNA barcoding鉴定的片段使用。
[Objective]Sequence character of nrDNA ITS2 fragment in Bupleurum scorzonerifolium Willd. was analyzed to provide scientific evidence in identification of traditional Chinese medicinal herb chaihu.[Method]Forty-one sequences including thirty-eight full length ITS and three ITS2 fragments were downloaded from GenBank.Nucleotide composition,variable sites,parsimony informative sites were analyzed after alignment in MEGA6.0.Meanwhile,the genetic distances were computed using Kimura-2-parameter(K2 P) model and phylogenetic tree was constructed using the neighbor-joining(NJ) method.[Result]The length of ITS2 varied from 224 bp to 230 bp including 14 parsimony informative sites,and the maximum K2 P distance was 0.124.Four clades were grouped in NJ tree among which 85.37% sequences clustered in clade IV.[Conclusion]ITS2 is an ideal sequence in chaihu identification for its conservatism among B.scorzonerifolium populations.
[Objective]Sequence character of nrDNA ITS2 fragment in Bupleurum scorzonerifolium Willd. was analyzed to provide scientific evidence in identification of traditional Chinese medicinal herb chaihu.[Method]Forty-one sequences including thirty-eight full length ITS and three ITS2 fragments were downloaded from GenBank.Nucleotide composition,variable sites,parsimony informative sites were analyzed after alignment in MEGA6.0.Meanwhile,the genetic distances were computed using Kimura-2-parameter(K2 P) model and phylogenetic tree was constructed using the neighbor-joining(NJ) method.[Result]The length of ITS2 varied from 224 bp to 230 bp including 14 parsimony informative sites,and the maximum K2 P distance was 0.124.Four clades were grouped in NJ tree among which 85.37% sequences clustered in clade IV.[Conclusion]ITS2 is an ideal sequence in chaihu identification for its conservatism among B.scorzonerifolium populations.
引文
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[13] 王长宝,马祥光,何兴金.对东亚广义三岛柴胡的再认识及GenBank中几个有疑问nrDNA ITS序列的评价[J].江苏师范大学学报(自然科学版),2013,31(1):64-73.
[2] 中国科学院植物志编辑委员会.中国植物志:第55卷[M].北京:科学出版社,1979:95-215.
[3] 王川易,郭宝林.植物核基因组核糖体基因间隔区序列的结构特点及其在系统发育研究中的应用[J].武汉植物学研究,2008,26(4):417-423.
[4] 李学营,彭建营,白瑞霞.基于核 rDNA的 ITS 序列在种子植物系统发育研究中的应用[J].西北植物学报,2005,25(4):829-834.
[5] VIJAYAN K,TSOU C H.DNA barcoding in plants:Taxonomy in a new perspective [J].Current science,2010,99(11):1530-1541.
[6] 罗焜,陈士林,陈科力,等.基于芸香科的植物通用 DNA 条形码研究[J]. 中国科学:生命科学,2010,40(4):342-358.
[7] YAO H,SONG J Y,LIU C,et al.Use of ITS2 region as the universal DNA barcode for plants and animals [J].PLoS One,2010,5(10):1-9.
[8] PANG X H,SHI L C,SONG J Y,et al. Use of the potential DNA barcode ITS2 to identify herbal materials [J]. Journal of natural medicines,2013,67(3):571-575.
[9] 李栎,肖憬,苏振宇,等.ITS2 条形码序列对茜草科黎药植物的鉴定[J]. 中草药,2013,43(13):1814-1818.
[10] 侯典云,宋经元,石林春,等. 中药材锁阳的 ITS2 条形码分子鉴定研究[J]. 中国中药杂志,2013,38(23):4028-4032.
[11] BURLAND T G.DNASTAR's Lasergene sequence analysis software[M]//MISENER S,KRAWETZ S A.Bioinformatics methods and protocols.Totowa,New Jersey:Humana Press,2000.
[12] LEWIS P O,KUMAR S,TAMURA K,et al. MEGA6:Molecular evolutionary genetics analysis version 6.0[J].Molecular biology & evolution,2013,30(12):2725-2729.
[13] 王长宝,马祥光,何兴金.对东亚广义三岛柴胡的再认识及GenBank中几个有疑问nrDNA ITS序列的评价[J].江苏师范大学学报(自然科学版),2013,31(1):64-73.